+ ACC=AF086833
+ SRR=SRR1972739
+ N=10000
+ REF=refs/AF086833.fa
+ mkdir -p refs
+ efetch -db=nuccore -format=fasta -id=AF086833
+ bowtie2-build refs/AF086833.fa refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ fastq-dump -X 10000 --split-files SRR1972739
+ R1=SRR1972739_1.fastq
+ R2=SRR1972739_2.fastq
+ bowtie2 -x refs/AF086833.fa -1 SRR1972739_1.fastq -2 SRR1972739_2.fastq
+ cat SRR1972739.sam
+ samtools sort
+ samtools index SRR1972739.bam
+ samtools flagstat SRR1972739.bam